c57_nos2KO_mouse_countDF <- assign_hierarchy(c57_nos2KO_mouse_countDF, TRUE, "KEGG")
c57_nos2KO_mouse_countDF <- c57_nos2KO_mouse_countDF[1:20,]
t_test_df <- omu_summary(count_data = c57_nos2KO_mouse_countDF,
metadata = c57_nos2KO_mouse_metadata,
numerator = "Strep", denominator = "Mock", response_variable = "Metabolite",
Factor = "Treatment",
log_transform = TRUE, p_adjust = "BH", test_type = "welch")
fold_change_counts <- count_fold_changes(count_data = t_test_df,
column = "Class", sig_threshold = 0.05, keep_unknowns = FALSE)
ra_table <- ra_table(fc_data = fold_change_counts, variable = "Class")
pie_chart(ratio_data = ra_table, variable = "Class", column = "Decrease", color = "black")
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